1. Molecular Modeling: The Computer is the Lab
Niels Johan Christensen
IGM/Bioinorganic Chemistry/NP3 centre

2. Overview
Brief intro to molecular modeling
Molecular modeling at the NP3 centre: Application to novel insulin complexes
Clustering
Acknowledgements
Questions

3. What is Molecular Modeling?
Wikipedia´(
Molecular modelling encompasses all theoretical methods and computational techniques used to model or mimic the behaviour of molecules. The techniques are used in the fields of computational chemistry, computational biology and materials science for studying molecular systems ranging from small chemical systems to large biological molecules and material assemblies…. inevitably computers are required to perform molecular modelling of any reasonably sized system….
Andrew R. Leach, ”Molecular modelling, principles and applications”, second edition:
…we shall not concern ourselves with semantics but rather shall consider any theoretical or computational technique that provides insight into the behaviour of molecular systems to be an example of molecular modelling.

4. The Molecular Modeling Toolbox
Molecular Mechanics Methods
Molecules modeled as spheres (atoms) connected by springs (bonds)
Fast, >106 atoms
Limited flexibility due to lack of electron treatment
Quantum Mechanical Methods
Molecules represented using electron structure (Schrödinger equation)
Computationally expensive , < atoms, depending on method
Highly flexible – any property can in principle be calculated
Typical applications
Simulating biomolecules in explicit solvent/membrane
Geometry optimization
Conformational search
Chemical reactions
Spectra
Accurate (gas phase) structures, energies

5. The insulin project at the NP3 centre*
Synthesis: Engineered insulin with a novel metalion binding-site
Experimental data: CD, UV-vis
Goal: Elucidate the structure of a the novel insulin-complex in solution
Molecular modeling methodologies employed:
Molecular mechanics
Molecular dynamics
Quantum mechanics (Density functional theory) *

6. Prelude: Isomers of a (2,2’)-bipyridine Fe(II) complex 
Facial (fac)
 -fac
-fac
Meridional (mer)
-mer
 -mer

7. Circular dichroism
Measures differential absorption of left and right circularly polarized light by chiral molecules
Only CD can establish the absolute configuration of molecules in solution
Image source:

8. Engineered insulin as a building block in bionanotechnology
Hexamer of native insulin. Zinc (grey sphere) coordinated by HisB10 (green licorice)
Monomers of engineered insulin: Bipyridine has been introduced at position A1 (left) or B29 (right). HisB10 is also shown
Insulin chain figure from :

9. [Fe( )3]2+ Which species dominate in solution?
Three bipy-functionalized insulins form 4 distinct complexes with iron(II). Here, B29 functionalized insulin (similar for A1):
[Fe( )3]2+
 -fac
-fac
-mer
-mer
Which species dominate in solution?

10. Circular Dichroism – calculated vs measured
QM calculations on truncated systems (inset), measurements on B29 and A1 engineered insulin trimers in solution with Fe(II)
-fac
Erel(QM) = 0.0kJ/mol
-fac
Erel(QM) = 0.0 kJ/mol
Calculated
Calculated
B29
B29 A1 A1
Measured
Measured
-mer
Erel(QM) = 2.1 kJ/mol
-mer
Erel(QM) = 2.1 kJ/mol
Calculated
Calculated

11. Circular Dichroism – calculated vs measured
Comparison of measured/calculated CD sign changes allows determination of enantiomer dominating in solution: A1 (), B29 ()
Meridional (mer) and facial (fac) configuation cannot be firmly established from CD alone.
Energies from a conformational search on (truncated) systems may help in determining fac/mer preferences

12. Conformational search on a truncated B29 trimer
Conformational search: [Fe(bipy)3]2+ core fixed, rotate remaining groups systematically to find lowest energy:
 -fac
0.0 kJ/mol
-fac
14.3 kJ/mol
-mer
25.4 kJ/mol
-mer
30.0 kJ/mol

13. Molecular dynamics simulations can be used to elucidate the dynamics of biomolecules
Example: Rearrangement of an engineered insulin monomer

14. Clustering: Building a larger calculator

15. Acknowledgements
Henrik K. Munchb, Søren Thiis Heidea, Thomas Hoeg-Jensenc, Peter Waaben Thulstrupa and Knud J. Jensenb
a Bioinorganic Chemistry, Department of Basic Sciences and Environment, Faculty of Life Sciences, University of Copenhagen, Denmark
b Bioorganic Chemistry, Department of Basic Sciences and Environment, Faculty of Life Sciences, University of Copenhagen, Denmark
c Novo Nordisk , Maaloev, Denmark
Det Strategiske Forskningsråds Programkomite for Nanovidenskab og -teknologi, Bioteknologi og IT (NABIIT)